← Back to search

1ek5

STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+

Method: X-RAY DIFFRACTION D_max: 64.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1ek5
deposition_date	2000-03-06
title	STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+
keywords	Short-Chain Dehydrogenase, Epimerase, Galactosemia, ISOMERASE; ISOMERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.54 Å
rg_electron	19.55 Å
i0	26121300.00
molecular_weight	38694.0 kDa
excluded_volume	48177 Å³
envelope_volume	55097 Å³
shell_volume	22988 Å³
envelope_diameter	66.6 Å
shell_rg	26.60 Å
envelope_rg	19.78 Å
shape_rg	19.54 Å
total_rg	20.47 Å
total_atoms	2719
n_residues	346
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	64.7 Å
rg_real	20.43 Å
rg_real_error	0.26 Å
i0_real	2.6120e+07
i0_real_error	2.9030e+05
rg_reciprocal	20.45 Å
i0_reciprocal	26120000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.205
kurtosis	-0.333
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	7450000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.997

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	UDP-GALACTOSE 4-EPIMERASE
formula_weight	38324.6 kDa
ec_number	5.1.3.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2915

MAEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGTQA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	196

▶

6. Citations (1)

▶

length_a	50.300 Å
length_b	116.400 Å
length_c	130.400 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.800 Å
resolution_low	30.000 Å
r_factor	0.1910
r_work	0.1900
r_free	0.2230

fit	/app/data/saxs_computation/ek/1ek5/1ek5.fit
pddf	/app/data/pr_computation/ek/1ek5/1ek5.pr.out
profile	/app/data/saxs_computation/ek/1ek5/1ek5.dat

STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction